imodfillin(1) General Commands Manual imodfillin(1)
NAME
imodfillin - fill in missing contours in IMOD model or remove inside
contours
SYNOPSIS
imodfillin [options] input_model output_model
DESCRIPTION
Imodfillin will fill in contours in an IMOD model on sections that were
skipped during modeling, or remove contours that are inside others
(filling in the inside in another sense). For the filling operation,
it interpolates a contour between existing ones using information in
the object mesh created by Imodmesh or 3dmod. Each interpolated
contour will fall on the surface connecting existing contours. It is
thus necessary to get objects meshed before running imodfillin. Since
you need to have a mesh between contours on non-adjacent sections, you
should use one or more meshing options to connect across gaps in the
data. If sections have either a complete set of contours or no con-
tours at all, then the -s (Skip) option will suffice. If the pattern
is less rigid than this, use the -P (Passes) option in addition (or
exclusively), where the number of passes that you specify with this
option equals the maximum number of sections of separation between con-
tours that you wish to connect. Do not use any Imodmesh option that
would set the z increment to greater than 1 (i.e., -l, -i, or -z (Z inc
in 3dmod), for then Imodfillin will probably create contours on sec-
tions that already have them.
Objects containing meshes from an isosurface and no contours will be
analyzed differently to extract contour trajectories from lines in the
mesh that lie exactly on Z planes. It does not interpolate between
these planes, so if the isosurface is made with binning, the contours
will not be on every Z plane. Parts of the surface that are cut off by
the bounding box will result in open contours. Some of these may have
gaps in them, but closed contours should generally be complete. The
resulting contours are unlikely to mesh properly except for compact,
well-separated surfaces. The default point reduction with a tolerance
of 0.25 pixel may be too high for isosurfaces around small structures.
By default, the program will attempt to fill in all closed-contour
objects that have meshes, but will skip open-contour objects. Use the
-o option to specify a subset of objects to be done, or to force it to
do particular open-contour objects.
The created contours will inherit any surface or time information con-
tained in the meshes. If your original contours have surface numbers,
be sure to mesh with the -S option to preserve this surface information
in the meshes, so that the interpolated contours will have the same
surface numbers as the original ones.
The removal of inside contours is activated by the -I option, which
specifies whether to remove just contours at even levels (i.e., inside-
facing ones) or all interior contours. In this case, the other options
have no effect, except -o to specify a list of objects and -z to
restrict the range of Z values over which the removal happens.
OPTIONS
-e Place new contours in existing objects. Use this option if you
do not plan to check and modify the interpolated contours.
-n Place new contours in new objects; this is the default, so that
contours can be checked conveniently. One new object will be
created for each object that is being filled in. These contours
may be moved into the proper object either one by one or all at
once via the Edit-Contour-Move dialog and M hotkey in 3dmod.
-o list
Do operations only on objects in the list of numbers. The list
can consist of comma-separated ranges (e.g., 1,7-11,13-17,19).
Without this option, all closed contour objects with meshes are
filled in.
-i value
Set the Z increment for filling in contours. This option has
two effects: the program will fill in only gaps that are wider
than the given value, and it will insert new contours at this
given Z increment instead of on every section.
-R value
Resolution or tolerance for point reduction in the generated
contours. Points are eliminated if they are within this dis-
tance of the lines connecting the remaining points, just as with
the -R option in Imodmesh. Values in the range 0.25 to 0.5
are often useful; the default is 0.25.
-I value
Enter 2 to remove all contours contained inside other contours,
or 1 to remove contours that are immediately inside an outward-
facing one, i.e, ones that constitute the inside surface of a
donut-shaped object.
-z start,end
Range of Z values (numbered from 0) within which to remove con-
tours when the -I option is entered.
FILES
If the model file already exists, it becomes a backup file with ~ added
to its name.
AUTHOR
David Mastronarde
SEE ALSO
3dmod, Imodmesh
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.12.61 imodfillin(1)